Methods and compositions for high throughput identification of protein/nucleic acid binding pairs

• US 7,192,710 B2
• Filed: 03/29/2004
• Issued: 03/20/2007
• Est. Priority Date: 06/25/2002
• Status: Expired due to Fees

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Leproust, Eric M., Gellibolian, Robert
• Primary Examiner(s): Kim; Young J.
• Application Number:
  US10/813,639
• Publication Number:
  US 20050003395A1
• Time in Patent Office: 1,086 Days
• Field of Search: None
• US Class Current: 435/6.1
• CPC Class Codes: B01J 2219/00378 Piezoelectric or ink jet dispensers
• CPC Class Codes: B01J 2219/00387 Applications using probes
• CPC Class Codes: B01J 2219/00497 Features relating to the solid phase supports
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00576 fluorophore
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/0063 Other, e.g. van der Waals forces, hydrogen bonding
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00677 Ex-situ synthesis followed by deposition on the substrate
• CPC Class Codes: B01J 2219/00707 separated from the reactor apparatus
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00729 Peptide nucleic acids [PNA]
• CPC Class Codes: C12Q 1/6818 involving interaction of two or more labels, e.g. resonant energy transfer
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2561/101 Taqman
• CPC Class Codes: C12Q 2565/531 : characterised by the capture moiety being a protein for target oligonucleotides
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 60/14 : for creating libraries

Abstract

Methods and compositions for high-throughput identification of protein/nucleic acid binding pairs are provided. In the subject methods, a nucleic acid probe array, e.g., a molecular beacon probe array, is contacted with a target nucleic acid population to produce a hybridized array. The resultant hybridized array is then contacted with a population of proteins to produce a protein bound array. Any resultant array surface bound target nucleic acid/protein complexes are then detected to identify protein/nucleic acid binding pairs. In certain embodiments, the protein and/or nucleic acid members of the identified protein/nucleic acid binding pairs are further characterized. Also provided are systems and kits for use in practicing the subject methods. The subject invention finds use in a variety of different applications.

Claims

1. A method of identifying protein/nucleic acid binding pairs, said method comprising:

(a) contacting a target nucleic acid contacted molecular beacon array comprising a plurality of distinct molecular beacon probes, wherein each distinct probe of said plurality comprises a different probe sequence and all of said probes of said plurality share a common first fluorescent label, with a population of fluorescently labeled proteins to produce a protein bound array, where each member of said population of fluorescently labeled proteins is labeled with a second fluorescent label that makes up a FRET pair with said first fluorescent label; and

(b) detecting any FRET generated signals from said array to identify protein/nucleic acid binding pairs on said array.

2. The method according to claim 1, wherein said method further comprises characterizing the protein of a protein/nucleic acid binding pair identified by said method.

3. The method according to claim 1, wherein said method further comprises characterizing the protein binding sequence of a nucleic acid of a protein/nucleic acid binding pair identified by said method.

4. The method according to claim 1, wherein said array is contacted with two differentially labeled protein populations.

5. The method according to claim 4, wherein said two differentially labeled protein populations make up a test/control pair.

6. The method according to claim 4, wherein said two differentially labeled protein populations make up a normal/disease pair.

7. The method according to claim 1, wherein said method further comprises a data transmission step in which a resutt from a reading of the array is transmitted from a first location to a second location.

8. The method according to claim 7, wherein said second location is a remote location.

9. A method of identifying protein/nucleic acid binding pairs, said method comprising:

(a) contacting a target nucleic acid contacted molecular beacon array comprising a plurality of distinct molecular beacon probes, wherein each distinct probe of said plurality comprises a different probe sequence and all of said probes of said plurality share a common first fluorescent label, with at least one fluorescently labeled protein to produce a protein bound array, where said at least one fluorescently labeled protein is labeled with a second fluorescent label that makes up a FRET pair with said first fluorescent label; and

(b) detecting any FRET generated signals from said array to identify protein/nucleic acid binding pairs on said array.